file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 39.0 42.0 43.0 42.9 44.0 45.0
## [1] 40
## [1] 39 40 41 41 41 41 41 41 41 42 42 42 42 42 43 43 43 43 43 43 43 43 44 44 44
## [26] 44 44 44 44 44 44 44 44 44 44 44 45 45 45 45
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
##
## FALSE TRUE
## 1643 357
##
## FALSE TRUE <NA>
## 21 1622 357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 6900 0.118699020 90.14412
## 2: gene 161 0.002485395 99.77003
## total_counts
## 1: 8310
## 2: 174
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00857 90.44551 99.20296 90.72478 99.93429 100.00000
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 60.04 81.87 72.81 92.88 97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: A2M A2M A2M ENSG00000175899 FALSE
## 2: A2ML1-AS1 A2ML1-AS1 A2ML1-AS1 ENSG00000256661 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 5826 0.1207987
## 2: NCBITaxon:9606 gene 11030 0.2138297
## pct_dropout_by_counts total_counts selected
## 1: 91.67821 8457 1
## 2: 84.24488 14970 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MYO16" "AMPH" "PPEF1" "SGK2" "FRK" "SIPA1L2"
## [7] "APOC1" "MON1A" "CES2" "ZNF497" "RAB39A" "IL1RAPL2"
## [13] "ITGA3" "CCDC124" "SYN1" "NGEF" "PPP1R15A" "CASS4"
## [19] "EPHB6" "SUSD1" "CHD5" "DUSP1" "KIAA1217" "LRRC4B"
## [25] "HAVCR2" "MICAL1" "ARHGAP26" "SNTG1" "SLC43A1" "TBX6"
## [31] "FSIP1" "CNKSR3" "FBXO32" "C2CD2" "DHRSX" "REPS2"
## [37] "SYNM" "ANKS1B" "HAUS7"
## [1] 2
## [1] "ANKRD24" "SPATA6L" "TFAP2E" "DNAH12"
## [5] "HDHD5-AS1" "MAMDC2-AS1" "LEFTY1" "RP11-1252I4.2"
## [9] "RP4-785G19.5" "RP11-20I20.2" "IDH2-DT" "RP11-396B14.2"
## [13] "SYNPO2L-AS1" "RP5-965G21.3" "P2RX7" "CATSPERG"
## [17] "AGFG2" "NKD1" "GAL3ST2" "ADCY8"
## [21] "CFAP251" "ZNF653" "DHRS3" "C2"
## [25] "TVP23A" "NAV2" "GNG4" "C7orf61"
## [29] "CCDC30" "TRPV1" "LINC00862" "DISP3"
## [33] "ODAD4" "ARL17B" "RP11-348F1.3" "LINC00342"
## [37] "LINC00884" "LINC01137" "EPCAM-DT" "KCNK15-AS1"
## [41] "RP11-60A24.3" "CTD-2189E23.1" "RP11-465L10.14" "RP11-125C10.1"
## [1] 3
## [1] "NRXN3" "RPH3A" "PEX5L" "UNC13A"
## [5] "CALY" "NDST3" "GRIK2" "FSTL5"
## [9] "NRG4" "MTSS1" "GRIK1" "NEGR1"
## [13] "ERICH3" "CCSER1" "NAP1L3" "CYP4X1"
## [17] "PCLO" "ERC2" "GRM7" "FBXO16"
## [21] "RP11-170M17.1" "MSC-AS1" "CXXC4-AS1" "LINC02217"
## [25] "RP4-809F18.1" "RP11-413N10.3" "RP11-640F22.1" "RP11-320L2.1"
## [29] "RP11-335E8.3" "RIMS1" "SEC14L5" "PDE1A"
## [33] "RIMS3" "NLGN1" "RIMS2" "SYN3"
## [37] "PTPRT" "MMP17" "CYP1B1-AS1" "RP11-147G16.1"
## [41] "LINC01322" "PCAT1" "RP11-4D11.1"
## [1] 4
## [1] "BID" "FAR2" "SRPX" "CLIC5" "CRISPLD1" "EEPD1"
## [7] "MASP1" "FADS2" "PTH1R" "IGFBP7" "HESX1" "METTL2B"
## [13] "TMEM130" "GPC6" "ARHGAP8" "PTPRN" "EBF4" "DOK5"
## [19] "RASL12" "BNIP3L" "KLHL29" "NCAN" "GFPT2" "ARID5B"
## [25] "KCNE4" "MYO1E" "SPTBN4" "OXR1" "ABCA3" "KIF5C"
## [31] "CLIC4" "IFFO2" "NPAS2" "PFKFB3" "FRMD5" "RGMA"
## [37] "DUSP8" "ZBTB7C" "TRDN" "RASGEF1A" "RNF208"
## [1] 5
## [1] "MAMLD1" "HHAT" "AHRR" "MROH8"
## [5] "PEBP4" "EFCAB11" "GULP1" "KIAA1328"
## [9] "ZBTB44-DT" "CASC2" "RFLNA" "COL25A1"
## [13] "RFX8" "FIRRE" "LIPE-AS1" "LINC02649"
## [17] "AC105760.2" "TARID" "AC008269.2" "COX10-AS1"
## [21] "RP11-550I24.2" "DRAIC" "CTB-161M19.4" "LINC02615"
## [25] "RP11-266O8.1" "SPESP1" "RP11-111A21.1" "CRTC3-AS1"
## [29] "GEMIN7-AS1" "PLS3-AS1" "RP11-96C13.1" "RP4-681L3.3"
## [33] "NIPAL3" "DOCK10" "NRG2" "FAAH2"
## [37] "TMEM229B" "WARS2-AS1" "LINC01135" "DPH6-DT"
## [41] "AC079610.1" "RP11-379B18.8" "RP11-799O21.2"
## [1] 6
## [1] "SNCAIP" "MAOB" "SEMA3A" "SYTL4"
## [5] "IQCH" "DPYSL3" "TACR1" "LEPR"
## [9] "ACAT2" "COL4A2" "ABI3BP" "PRTG"
## [13] "VWA3B" "HEG1" "PROS1" "F5"
## [17] "LRRC24" "RNF19A" "SEMA3C" "PIR"
## [21] "SPAG1" "FGL1" "ST8SIA1" "MAN1A1"
## [25] "UST" "SERPINI2" "PRRX1" "COL21A1"
## [29] "PRR12" "FCHO1" "COL6A2" "LMNTD1"
## [33] "SEMA3D" "DPYSL5" "ELAPOR2" "TMC1"
## [37] "NPNT" "ZFP36L1" "CPEB1" "RP11-190P13.2"
## [41] "CTD-2054N24.2"
## [1] 7
## [1] "CAP2" "TACC2" "FAXC"
## [4] "LMOD1" "NXN" "SLC43A2"
## [7] "CCBE1" "C9orf153" "TRMT9B"
## [10] "MAP3K9" "GTF2IRD1" "HDAC9"
## [13] "PDZD4" "MYO9B" "SYT17"
## [16] "ARHGEF18" "AEBP1" "WASF1"
## [19] "PACRG" "IL1R1" "ZC4H2"
## [22] "HIP1" "ZBTB46" "IRAK2"
## [25] "KIAA0513" "CCDC40" "MVB12A"
## [28] "CLVS2" "RHPN1" "TMCO4"
## [31] "PIK3CD" "MOB3A" "HAP1"
## [34] "RILPL1" "COL27A1" "NHSL2"
## [37] "MEF2B" "LYRM4" "RP11-513I15.6"
## [40] "FBXO17" "DGCR5_ENSG00000273032" "CASTOR2"
## [1] 8
## [1] "ZFR2" "ST6GALNAC5" "CABLES1" "ABHD3"
## [5] "ANKRD33B" "ADRA1B" "HOPX" "TAFA1"
## [9] "SLIT1" "SULT1A2" "PPP1R26-AS1" "RP11-390F4.6"
## [13] "RP11-380P13.1" "MTRNR2L8" "AC005786.7" "ADGRL1"
## [17] "TRHDE" "CACNA1I" "XYLT1" "PADI2"
## [21] "TGIF2" "TICAM1" "RAP1GAP2" "RHBDL3"
## [25] "ADAMTS10" "ST3GAL2" "CSDC2" "GNG7"
## [29] "CTD-2527I21.15" "SPACA6" "OSBP2" "NOTUM"
## [33] "AJAP1" "NRSN2-AS1" "HPN-AS1" "AC004951.6"
## [37] "HMGA1P4" "RP5-827C21.2" "RP11-346L1.2" "LINC02356"
## [41] "RP3-414A15.10" "MAFG-DT" "ATP6V0D1-DT" "RP11-514P8.10"
## [1] 9
## [1] "EPHA6" "ENOX1" "UNC79" "TMEM132B"
## [5] "C4orf19" "MN1" "ANO5" "MACROD2"
## [9] "LRRC3B" "APTR" "LCNL1" "AP001628.6"
## [13] "RP11-498J9.2" "OBI1-AS1" "RP11-410D17.2" "CTC-329D1.2"
## [17] "LINC01950" "RP11-582J16.4" "LINC00923" "MGAM"
## [21] "RP11-524F11.2" "CTD-2349P21.11" "RP11-437L7.2" "RP11-1289C17.1"
## [25] "RP11-215I16.3" "ATP1A2" "RNF24" "TENM2"
## [29] "ENOX2" "ZMAT3" "ARPP21" "EFNA5"
## [33] "PLK5" "TPCN1" "C3orf35" "RP11-305L7.3"
## [37] "KCNMB2-AS1" "RP5-921G16.1" "LINC01252" "RP11-298I3.1"
## [41] "AGBL1" "RP11-711K1.8"
## [1] 10
## [1] "TRPM3" "GALNT16" "EFEMP1" "GTDC1" "TMEM108" "CXCL14"
## [7] "ACSL1" "WIF1" "VWCE" "TMEM51" "RNLS" "KLHL32"
## [13] "BRINP2" "RARB" "TGFB2" "PALM" "MYOM1" "EEF2K"
## [19] "KAT8" "PPP1R13L" "ISYNA1" "PPARGC1A" "TPD52L1" "TFDP2"
## [25] "B4GALT2" "FOXO3" "SLC39A11" "VAV3" "CCNH" "TIAM2"
## [31] "FAM171A1" "ZEB1" "CNNM2" "FOXO1" "FAM107A" "ZNF608"
## [37] "CRADD" "TCAP" "PARVA" "ZNF358" "EFCAB2" "EML6"
## [1] 11
## [1] "CD38" "REEP1" "SP140" "ANKRD7"
## [5] "PLAGL1" "H3-3B" "BEND6" "BTG2"
## [9] "VWA3A" "PLD5" "PRELID2" "SLC4A5"
## [13] "LGALSL-DT" "LINC01630" "RP11-106M7.1" "LINC00407"
## [17] "CDKN2B-AS1" "BAALC-AS1" "LINC02234" "C5orf17"
## [21] "OSMR-AS1" "RP11-157I4.4" "MPPED2-AS1" "RP11-363J20.2"
## [25] "RP11-798K3.2" "LINC00907" "CTC-513N18.6" "RP11-355F16.1"
## [29] "LINC01374" "ARRDC3-AS1" "BCL6-AS1" "CTD-2313D3.2"
## [33] "RP11-125D12.3" "RP11-592G13.2" "RP11-341N18.1" "TLE2"
## [37] "USP9Y" "PDPN" "NLGN4Y" "TTTY14"
## [41] "UTY" "TTTY10" "RP5-1198O20.4" "LINC00278"
## [1] 12
## [1] "KIRREL3" "GALNTL6" "LINC00326" "KIF5C-AS1"
## [5] "CTD-2126E3.6" "SYT7" "KLHL4" "ATRNL1"
## [9] "SCN2A" "UNC13C" "AK7" "CBLN2"
## [13] "SLC4A10" "CDH18" "CNTN5" "ZNF385D"
## [17] "SLC24A2" "CFAP161" "SHROOM4" "LRRC2"
## [21] "HTR1E" "SLC38A11" "SEMA3E" "SLC8A1"
## [25] "KCNH7" "RTN4RL1" "PDE2A" "CACNA1E"
## [29] "TNFRSF25" "AC023469.1" "RP11-191L9.4" "RP1-30E17.2"
## [33] "RP11-563D10.1" "KRTAP5-AS1" "AC067956.1" "SHISA9"
## [37] "AC002066.1" "CTC-340A15.2" "LINC02223" "RP11-79E3.2"
## [41] "RP11-624C23.1" "RP11-958J22.1" "RP11-596C23.6" "IQCJ-SCHIP1"
## [1] 13
## [1] "ATP11A" "MAP2K6" "MGAT3" "PRR5L" "FAM117B"
## [6] "SLC44A3" "C4orf45" "PBX3" "LRRN2" "CTA-292E10.6"
## [11] "HGF" "SAMD4A" "APBA2" "CDON" "PDK3"
## [16] "TMEM38A" "ITPKC" "RELB" "OLFM2" "PLIN3"
## [21] "RFTN1" "ZSWIM4" "NFIC" "ENSA" "BOC"
## [26] "ZNF208" "FBXO27" "SHISA5" "PKNOX2" "FRMD3"
## [31] "SYT12" "PACS1" "CMTM4" "DMWD" "TCEA3"
## [36] "LINC00685" "RP5-864K19.4" "L3MBTL2-AS1" "OLMALINC" "RP1-158P9.2"
## [41] "MIR23AHG" "RP11-404C6.6"
## [1] 14
## [1] "UPP2" "MOGAT1" "DPH6" "CD72"
## [5] "MAP3K7CL" "RHCE" "CRPPA" "POT1-AS1"
## [9] "LNC-LBCS" "LINC01185" "MIR181A1HG" "MMADHC-DT"
## [13] "RP11-120D5.1" "RPL34-DT" "NPIPB2" "SUCLG2-AS1"
## [17] "RP11-11N9.4" "RP11-130F10.1" "RP11-268P4.5" "RP11-284M14.1"
## [21] "LINC01182" "MAILR" "RP11-156K13.1" "RP11-20E24.1"
## [25] "RP11-397A16.1" "RP11-436D23.1" "RP11-281A20.2" "RP11-382N13.7"
## [29] "RP11-692P14.1" "RP11-444C24.1" "RP11-563M4.2" "CTD-2297M2.1"
## [33] "STAG1" "PDE3A" "LSMEM2" "AP000318.2"
## [37] "LINC00598" "AC104088.1" "ARHGEF26-AS1" "STX18-AS1"
## [41] "CASC17" "TAPT1-AS1" "RP11-26L21.1" "RP11-166M16.1"
## [1] 15
## [1] "PRKAR2B" "ARHGAP44" "TENM1" "ELAVL2" "MLIP" "SETBP1"
## [7] "SHANK2" "RGS7" "KCTD16" "SMYD3" "DLGAP2" "SYT1"
## [13] "RBFOX1" "UBE2R2" "ZMIZ1" "CPE" "HIVEP3" "QRICH2"
## [19] "DPP6" "SOX5" "TTLL7" "ZNF385B" "DIAPH2" "CACNA1B"
## [25] "SHANK1" "ABLIM2" "RBFOX3" "FRMPD4" "DLGAP1" "CNTNAP2"
## [31] "SAMD12" "RGS6" "CSMD1" "OPCML" "RALYL" "KCNQ5"
## [37] "KCNIP4" "ELAVL3" "ARID5A" "RYR2" "MEG3"
## [1] 16
## [1] "XK" "MAEL" "PAH" "GPR39"
## [5] "CC2D2B" "DCHS2" "DIO2" "RP11-306O13.1"
## [9] "AP000233.4" "LINC01117" "PLCG1-AS1" "AC012593.1"
## [13] "SOX21-AS1" "LINC01344" "AC007682.1" "LINC01937"
## [17] "AC009264.1" "RP11-142A5.1" "AC079305.11" "RP11-154H17.1"
## [21] "RP11-373N22.3" "LINC02144" "RP11-669M16.1" "RP11-679C8.2"
## [25] "RP11-404I7.2" "RP1-84O15.2" "LINC00534" "ZFHX4-AS1"
## [29] "RP11-804N13.1" "RP11-541P9.3" "RP11-431M3.1" "LINC02763"
## [33] "RMST" "RP11-260G13.1" "RP11-526N18.1" "RP11-242P2.1"
## [37] "CTC-498M16.4" "RP11-561I11.4" "LINC01727" "CH17-174L20.1"
## [41] "RP11-313M3.2" "RP3-383B8.1" "RP11-346I3.7" "AC006296.4"
## [45] "RP11-399K19.1"
## [1] 17
## [1] "MBNL3" "GABRA4" "HSD11B1" "HS3ST3B1" "GPNMB" "ABCA12"
## [7] "ARHGAP27" "AXDND1" "AGBL2" "ZCCHC18" "EPHX4" "C1QTNF4"
## [13] "SP140L" "WNT7B" "HES5" "L3MBTL3" "SAMD13" "BAALC-AS2"
## [19] "PDXP" "DCN" "ABCA7" "ZFY" "ANGPT2" "PCDH11Y"
## [25] "TNNT2" "TBX2" "AIF1L" "EDA2R" "C1QL1" "SLC6A6"
## [31] "FREM2" "KCNJ16" "CATIP" "SPATA2L" "ZER1" "LRRC8C"
## [37] "NXNL1" "MB21D2" "PCP4" "ETV5"
## [1] 18
## [1] "PNPLA3" "LYPD6B" "DPP10" "CNTN1" "RIMBP2" "CTNNA2"
## [7] "CAB39L" "TUSC3" "GLIS3" "CHRNE" "CLNK" "SGK1"
## [13] "PLXDC2" "HIF3A" "AHNAK" "GALNT8" "RIN2" "ARHGEF4"
## [19] "PLCE1" "SSH2" "BCAS3" "GABPB2" "KCNN3" "DOCK11"
## [25] "ITPRIP" "GRIK4" "RASSF3" "NCAM2" "ABR" "ZNF704"
## [31] "ABCA1" "WNK2" "SLC20A2" "FAM222B" "SH3PXD2B" "PPM1E"
## [37] "PHYHD1" "SWI5" "TSHZ2" "NHS" "SRGAP1" "S100A10"
## [43] "NEAT1"
## [1] 19
## [1] "WDR64" "GLIPR1L1" "FSIP2" "ANKUB1"
## [5] "RNF212B" "AC002463.3" "RP11-131L23.1" "RP4-660H19.1"
## [9] "RP11-547I7.1" "ST7-AS2" "ASTN2-AS1" "RP11-141A19.1"
## [13] "CCDC192" "GPC5-AS2" "PCDH9-AS4" "RP11-666F17.1"
## [17] "LINC02250" "AC008067.2" "RP11-475C16.2" "RP13-143G15.4"
## [21] "LINC02877" "LINC00960" "RP11-768G7.3" "RP11-115N4.1"
## [25] "LRP4-AS1" "ANK2-AS1" "RP11-223C24.1" "MAPK10-AS1"
## [29] "RP11-120A1.1" "RP11-116O11.1" "RP11-351A11.1" "RP11-463D19.1"
## [33] "RP11-513G19.1" "A2ML1-AS1" "RP11-370I10.2" "RP11-887P2.5"
## [37] "DIO2-AS1" "RP11-58G13.1" "RP11-138H11.1" "CTD-2282P23.2"
## [41] "CH17-140K24.2" "RP11-576O3.1" "RP11-394G3.3" "RP11-66G15.1"
## [1] 20
## [1] "PAPPA2" "MTERF1" "PKIB" "SAXO1"
## [5] "PKD1L1" "FREM1" "SCN11A" "RNF212"
## [9] "CLDN4" "SCOC-AS1" "LEKR1" "RP11-344B5.2"
## [13] "AC072062.3" "LINC00271" "RFX3-AS1" "AF131217.1"
## [17] "LINC01239" "LINC01524" "RP11-195C7.1" "LINC01376"
## [21] "LINC01695" "LINC02652" "RP11-132E11.2" "LINC01358"
## [25] "RP11-624M8.1" "H2AZ1-DT" "LINC02355" "LINC01340"
## [29] "LIX1-AS1" "C8orf37-AS1" "RP11-708B6.2" "RP11-511B23.2"
## [33] "RP11-352M15.1" "LINC02320" "RP11-16B13.1" "RP11-739G5.1"
## [37] "PSMD7-DT" "RP11-571L19.7" "RP11-157E16.1" "CTC-490G23.6"
## [41] "RP11-964E11.3" "RP11-274G22.1" "RP11-221G19.1" "RP5-892C22.1"
## [45] "RP11-446J8.1"
## [1] 21
## [1] "CALCRL" "CCDC80" "PLCB4" "SLC16A6"
## [5] "IFI44L" "SLC24A4" "ADAMTS9" "GUCY1A1"
## [9] "DELEC1" "CYP4F12" "CYP4F3" "STUM"
## [13] "INSYN2B" "RP11-735G4.1" "LINC01515" "LINC01768"
## [17] "DIRC3-AS1" "AC007563.5" "AC092684.1" "SOCS2-AS1"
## [21] "NEUROG2-AS1" "VCAN-AS1" "LINC02715" "MAP1LC3B2"
## [25] "RP11-116N8.1" "FRMD6-AS2" "PTCSC3" "DISC1FP1"
## [29] "RP11-793A3.2" "RP11-354K4.2" "RP11-323P17.2" "RP11-290O12.2"
## [33] "LINC00836" "LINC00842" "RP11-364P22.4" "RP11-373E16.6"
## [37] "RP11-259G3.1" "RP11-154D6.3" "RP11-609L3.3" "RP1-20N4.2"
## [41] "RP11-423B13.1" "RP11-469A15.2" "RP11-114N1.1"
## [1] 22
## [1] "PRKCQ" "SDK2" "CEMIP" "GBE1" "AKAP12"
## [6] "EPSTI1" "GALNT10" "STOX2" "CA8" "EXT1"
## [11] "CMSS1" "GCNT1" "TENM3" "MALAT1" "MCF2L2"
## [16] "PLXNA2" "KIF3C" "HSD17B14" "PCSK5" "NAMPT"
## [21] "LIN7A" "ZSWIM6" "ADGRB3" "ARHGAP29" "SLC44A5"
## [26] "PCSK6" "PTPRJ" "ABCB9" "THRB" "JAZF1"
## [31] "ADORA1" "PCDH7" "ALK" "CADM2" "NCKAP5"
## [36] "SLC25A20" "CADM1" "ABAT" "ARL15" "DNM3"
## [41] "TMEM161B-AS1"
## [1] 23
## [1] "CPED1" "BICC1" "SLC14A1"
## [4] "UNC5D" "LRRIQ3" "LINC01266"
## [7] "LMCD1-AS1" "AC097721.2" "LINC00877"
## [10] "RFX2" "SLC26A3" "DAAM1"
## [13] "CDH20" "STEAP1B" "LGI1"
## [16] "RFX4" "LRMDA" "PLCL2"
## [19] "GPR176" "GSG1L" "IQCK"
## [22] "PPP1R42" "APOLD1" "FIGN"
## [25] "LHFPL6" "MAML2" "FLRT2"
## [28] "FAM174B" "NKAIN2" "KIF9-AS1"
## [31] "LINC01320" "RP11-154D17.1" "RP11-17A1.3"
## [34] "LINC02742" "LINC01609" "RP11-20D14.3"
## [37] "RPPH1_ENSG00000259001" "LINC00558" "RP11-838N2.5"
## [40] "RMRP_ENSG00000269900" "CH507-528H12.1" "RP4-799O8.1"
## [43] "AC003099.2" "RP11-398J12.1"
## [1] 24
## [1] "CDH10" "EPB41L4B" "SCG3" "DHRS7B"
## [5] "SLC1A2" "DNAH7" "C10orf90" "MTCL1"
## [9] "SNTB1" "TMEM132C" "ROR1" "SHISA6"
## [13] "RP11-496B10.6" "ARHGAP31" "COL23A1" "RRP12"
## [17] "SYNE2" "DGKG" "SESN1" "PHACTR3"
## [21] "COBL" "CPEB3" "C1orf21" "WLS"
## [25] "PDZRN3" "TOX2" "TNS3" "SLC22A23"
## [29] "SHROOM3" "GLTP" "MAPK4" "SDK1"
## [33] "FAM13C" "ADAM33" "DOC2A" "PID1"
## [37] "GNA14" "AHCYL2" "CACNB2" "ZFPM2"
## [41] "ZNF785" "TOX"
## [1] 25
## [1] "PUDP" "RERG" "OTOGL" "SGCD"
## [5] "SLC24A3" "GRM3" "AC074391.1" "SOX1-OT"
## [9] "EPS15-AS1" "AP000282.2" "LINC01934" "LINC00886"
## [13] "HS3ST5" "LINC02196" "F11-AS1" "LINC00499"
## [17] "LINC01301" "RP11-317N12.1" "GS1-57L11.1" "RP11-134O21.1"
## [21] "LINC00540" "RP11-378A12.1" "RP11-624A4.2" "COL5A3"
## [25] "GRK3" "HPSE2" "CALCB" "FZD8"
## [29] "NME9" "ZNF98" "AC064875.2" "AC003991.3"
## [33] "SPRY4-AS1" "AC002127.4" "PDYN-AS1" "MEIKIN"
## [37] "RTL9" "ALDH1L1-AS2" "LINC02208" "LINC01414"
## [41] "RP11-328J6.1" "RP11-237N2.1" "RP11-421A16.1" "RP11-183J19.1"
## [1] 26
## [1] "IL7" "CA1" "LINC01931" "SHOC1"
## [5] "FILIP1L" "P2RY14" "HEPN1" "TMLHE-AS1"
## [9] "AC105461.1" "AC017101.10" "RP11-417B4.2" "GNA14-AS1"
## [13] "RP11-46O21.2" "GRM3-AS1" "LINC00513" "AC037445.1"
## [17] "RP11-109I13.2" "RBMS3-AS3" "STARD13-AS" "GS1-433O24.1"
## [21] "LINC01877" "RP11-657O9.1" "ZBTB20-AS5" "GK-AS1"
## [25] "RP11-274H2.2" "RORA-AS1" "LUCAT1" "RP11-39E3.3"
## [29] "ZFPM2-AS1" "STPG2-AS1" "CTD-3239E11.2" "BBOX1-AS1"
## [33] "CTD-2537O9.1" "RP11-1H15.2" "AP000462.2" "RP11-315E17.1"
## [37] "RP11-39M21.1" "CRIM1-DT" "PRKCA-AS1" "RP11-555K12.4"
## [41] "SLC5A11" "LINGO1" "LINC01208" "AC013463.2"
## [1] 27
## [1] "FAM107B" "SLC22A3" "RNF150" "LINC01876"
## [5] "XIST" "LINC02884" "CTXND1" "RP11-175O15.1"
## [9] "RASGRP2" "ARHGAP15" "RIPOR2" "TFCP2L1"
## [13] "ACVR1C" "SEM1" "IQCA1" "DMGDH"
## [17] "LGR6" "MRAS" "ESYT3" "VWA5B1"
## [21] "RFTN2" "RANBP3L" "PTCHD1" "FAXDC2"
## [25] "CHST11" "LDLRAD3" "SLC25A18" "POTEG"
## [29] "NWD1" "OSTN" "TMEM184B" "PLIN5"
## [33] "STARD10" "LINC00511" "DLEU2" "PTCHD1-AS"
## [37] "AC016745.3" "RP11-507B12.2" "RP11-507B12.1" "MTRNR2L12"
## [41] "CH507-513H4.1" "LINC02246" "RP11-358F13.1" "RP1-166D18.1"
## [1] 28
## [1] "WNT5B" "PDE10A" "F3" "GDAP1L1"
## [5] "TMEM241" "PDE5A" "MEGF11" "HHIP"
## [9] "SEPTIN1" "PNMA3" "SGCZ" "EYS"
## [13] "HES4" "NPSR1-AS1" "KCNMB2" "RP1-292B18.4"
## [17] "SNAP25-AS1" "RP1-45C12.1" "LINC01829" "LINC01618"
## [21] "RP11-673E1.1" "RP11-586K2.1" "AB015752.3" "LINC02389"
## [25] "LINC02254" "RP11-103J8.1" "RP11-314E10.1" "USH2A"
## [29] "RHOBTB1" "LAMB4" "WFDC1" "PXDNL"
## [33] "GREM1" "MRGPRF" "ZNF804B" "FZD9"
## [37] "HRAT92" "LINC02869" "RP11-384F7.1" "LINC01619"
## [41] "CEACAM16-AS1" "PKD1L3" "RP11-93B21.2"
## [1] 29
## [1] "PON3" "TENT5A" "AGBL3" "SLC9B1"
## [5] "C12orf42" "CATSPERE" "LINC01006" "RANBP17"
## [9] "COL28A1" "AC026188.1" "RP1-15D23.2" "HDAC2-AS2"
## [13] "PCDH9-AS2" "LINC01277" "CCDC26" "UFL1-AS1"
## [17] "PPP1R9A-AS1" "RNF217-AS1" "PKN2-AS1" "RP11-4B14.3"
## [21] "RP5-1101C3.1" "PTPRG-AS1" "NECTIN3-AS1" "RP11-167H9.4"
## [25] "MEF2C-AS2" "LINC00504" "RP11-436F23.1" "RP11-649G15.2"
## [29] "RP11-624D11.2" "CENATAC-DT" "PRANCR" "RP11-72M17.1"
## [33] "LINC01579" "RP11-525K10.3" "LINC01572" "TSIX"
## [37] "LINC02664" "RP11-470M1.2" "RP11-57G22.3" "RP11-69G16.2"
## [41] "RP4-660H19.2" "RP1-84D21.2" "RP11-120J1.2" "RP11-168F16.1"
## [1] 30
## [1] "PHACTR2" "FHAD1"
## [3] "HS3ST3A1" "PCED1B"
## [5] "RP1-167A14.2" "APP-DT"
## [7] "SLCO1A2" "CLIP2"
## [9] "JHY" "BEST3"
## [11] "PATJ" "TMTC1"
## [13] "TTC9" "DGKB"
## [15] "GMPR" "DENND2A"
## [17] "CCDC3" "LRGUK"
## [19] "DRC1" "ORAI2"
## [21] "SYTL3" "ADCY1"
## [23] "ARMC3" "DEPP1"
## [25] "PDZRN4" "TEKT1"
## [27] "ATOH8" "COL24A1"
## [29] "RCAN2" "PRIMA1"
## [31] "SPATA13_ENSG00000182957" "SHTN1"
## [33] "CFAP54" "LINC00632"
## [35] "S1PR3" "AC003090.1"
## [37] "AP001347.6" "AL163953.3"
## [39] "LINC02315" "LINC01094"
## [41] "ZNF594-DT" "KLF2-DT"
## [43] "RP11-35G9.5" "SCARNA2_ENSG00000270066"
## [45] "RP11-154H23.4"
## [1] 31
## [1] "NTN1" "SEZ6L" "SLC39A14" "RGS4" "TRIM5"
## [6] "TESPA1" "RNF165" "PLK2" "ARHGAP18" "PLEKHG4B"
## [11] "MMP16" "SYNPR" "FABP5" "KCNB2" "STAC3"
## [16] "PIWIL2" "AC011288.2" "KCNG1" "CDH3" "CELF4"
## [21] "SLC7A5" "MPP6" "TSPAN11" "NRP2" "SPP1"
## [26] "HS3ST2" "PMEPA1" "LOXL1" "SRRM4" "KCNH5"
## [31] "ITPR1" "RIT2" "FGF17" "PTMS" "ZMAT4"
## [36] "MAP1A" "VAT1L" "NABP1" "ST8SIA3" "VSTM2B"
## [41] "MTRNR2L1"
## [1] 32
## [1] "USH1C" "DNAH9" "GAB2" "SH3D19" "PPM1H" "UBE3D"
## [7] "BEX2" "BTBD11" "MIPOL1" "NDUFAF2" "ABTB2" "TSPAN5"
## [13] "ALCAM" "GPR156" "ADAP2" "AQP1" "SLC7A2" "PDE4A"
## [19] "ATP2B3" "RASAL2" "MAST3" "CDKL1" "COTL1" "SH3PXD2A"
## [25] "ARSB" "TMCC2" "NAV1" "CCDC146" "CDR2" "ITPKB"
## [31] "PAM" "MAGI1" "AKAP6" "ART3" "TIAM1" "GDPD5"
## [37] "ITGA2" "EDIL3" "PLEKHA7" "STX8" "SLC35E3" "ANO6"
## [43] "C19orf38"
## [1] 33
## [1] "CHODL" "STK32A" "BNC2" "LINC02814"
## [5] "RP11-364L4.3" "RP11-492O8.3" "ARHGAP6" "ST6GALNAC2"
## [9] "ST6GAL1" "FAP" "SOHLH2" "LRAT"
## [13] "KLF2" "CCDC175" "ANGPT1" "SAMD3"
## [17] "CFAP47" "PPP1R36" "METTL7B" "CAVIN1"
## [21] "PLCXD3" "SAMD11" "LAMA2" "PLPP4"
## [25] "CFI" "RP11-174G6.1" "RP1-111D6.3" "RP11-146I2.1"
## [29] "RP11-90C4.1" "IQCM" "LINC01411" "LINC01088"
## [33] "RP11-279O9.4" "LINC00609" "LINC02251" "RP11-259K15.2"
## [37] "RP11-627D16.1" "RP11-876N24.2" "RP1-79C4.4" "RP11-403A3.3"
## [41] "RP11-403A3.2" "RP11-542F9.2" "RP11-301F14.1" "RP11-6L16.1"
## [1] 34
## [1] "ASB4" "MSMO1" "CCDC85A" "IDI1" "SRBD1" "BLVRB"
## [7] "PLS3" "RPL18A" "EPM2A" "GMDS" "LAMA4" "ID2"
## [13] "NID1" "PPP1R3C" "MT2A" "ID1" "IFI6" "APOE"
## [19] "RPL36" "CCDC59" "RPLP1" "FAU" "TEX9" "GFRA1"
## [25] "SYCP2L" "HNF4G" "ALDH1A1" "RPS27" "ZNF48" "GINS3"
## [31] "KIAA0825" "MT1X" "PTMA" "SNHG31" "RPS18" "MRPL33"
## [37] "KNOP1" "ARID3A" "CKB" "MITF" "NOL4L"
## [1] 35
## [1] "MRC2" "RIPK2" "NT5DC3" "B3GAT2" "ADCY7" "EPHB2"
## [7] "AVIL" "LPAR4" "CCDC141" "CA3" "SVEP1" "SCG5"
## [13] "PAPPA" "CP" "ATP9A" "FOSL2" "GADD45B" "NFATC2"
## [19] "ABCC3" "IGSF21" "ID3" "ITIH5" "JUND" "EGF"
## [25] "CLSTN3" "DEPTOR" "ARHGAP35" "C1orf87" "ATF3" "TMEM200A"
## [31] "NFIL3" "NT5DC2" "JUNB" "SPSB1" "PLEKHG5" "RND1"
## [37] "PAWR" "YOD1" "FAM110C" "MAFF" "CRYBB2"
## [1] 36
## [1] "BCAS1" "SRPX2" "LRRC9" "LRTM1"
## [5] "CHST9" "CLMP" "MFSD4B" "DLEU1"
## [9] "COL5A2" "TSBP1" "Z83001.1" "RP4-613B23.1"
## [13] "DPP10-AS3" "AC009501.4" "IPO9-AS1" "GNG12-AS1"
## [17] "DPP10-AS1" "RP11-446H18.5" "SEMA6A-AS1" "RP11-114J13.1"
## [21] "CTD-2015H6.3" "RP11-348J24.1" "RP11-517I3.1" "RP11-711G10.1"
## [25] "RP11-452H21.1" "AP000487.6" "RP11-867G2.8" "RP11-144F15.1"
## [29] "RP11-104E19.1" "HIF1A-AS3" "RP11-184D12.1" "AC004158.3"
## [33] "RP11-80I3.1" "SLC7A14-AS1" "CTC-428H11.2" "RP11-589M4.5"
## [37] "RP11-793H13.14" "RP5-847G17.1" "CTD-2172F7.1" "RP11-725F23.1"
## [41] "RP11-255O19.2" "RP11-875G18.1" "NUP210L" "OVCH1"
## [45] "RP11-103P4.1"
## [1] 37
## [1] "ANOS1" "LRRC7" "KCNN2" "DNAH6"
## [5] "RGS22" "KCTD1" "LIX1" "SPATA17"
## [9] "KIF6" "JAM3" "ODAD2" "ENO4"
## [13] "MAML3" "MALRD1" "CHL1-AS2" "PATL2"
## [17] "RP1-232L24.3" "RP1-230L10.1" "CTC-347C20.1" "CTB-178M22.2"
## [21] "ADGRL1-AS1" "LINC00506" "RP11-574F11.4" "RP11-788A4.3"
## [25] "DNAH5" "MOB3B" "CNKSR2" "HNMT"
## [29] "FAM151B" "TDRD9" "FAT3" "SLC26A5"
## [33] "GPR137C" "PAX8-AS1" "TOGARAM2" "TSBP1-AS1"
## [37] "AC092155.4" "RP11-69I8.3" "RP1-35C21.2" "MIR4300HG"
## [41] "RP11-148E17.1" "RP11-210M15.2" "SPANXA2-OT1" "RP11-114N19.3"
## [1] 38
## [1] "MT3" "STS" "MT1G" "SUMF1"
## [5] "C2CD6" "STPG2" "CD200R1" "C11orf65"
## [9] "MT1E" "CYP7B1" "SUGCT" "HMGN5"
## [13] "ADD3-AS1" "MT1H" "AC007277.3" "AC004540.5"
## [17] "LINC00571" "MRPS9-AS2" "RP11-162D16.2" "LYPLAL1-DT"
## [21] "ZRANB2-AS2" "LINC01036" "AC079807.4" "RAP2C-AS1"
## [25] "RP11-154D6.1" "SOX2-OT" "RP11-461O7.1" "C1QTNF7-AS1"
## [29] "RP11-124B13.1" "LINC02740" "RP11-727A23.10" "LINC02745"
## [33] "LINC02326" "LINC02327" "LINC02328" "LINC00637"
## [37] "AC007193.6" "RP11-520F22.1" "KBTBD12" "RP11-26J3.1"
## [41] "RP11-150C16.1" "CTD-2201E18.6" "RP3-466I7.2"
## [1] 39
## [1] "SIDT1" "WSCD2" "ARHGAP28" "SLC8A3"
## [5] "KIAA1549L" "ELL2" "PLXNC1" "RNF175"
## [9] "DUSP15" "DNAAF1" "RETREG1" "GFRA2"
## [13] "SNX31" "DIRC3" "LINC01725" "LINC00958"
## [17] "MAPT-AS1" "MCUB" "BAIAP3" "VCAN"
## [21] "KITLG" "P3H2" "CCL2" "MAN1C1"
## [25] "SCN1A" "ST18" "PARP8" "NFASC"
## [29] "ARHGEF3" "SLITRK5" "FBN1" "TPST1"
## [33] "SLCO3A1" "CHST6" "XXbac-BPG55C20.7" "SATB1-AS1"
## [37] "CTD-2643I7.5" "PTCHD4" "CTB-35F21.1" "LINC02506"
## [41] "RP11-499F3.2" "AF038458.3" "RP5-1015P16.1"
## [1] 40
## [1] "RRAGD" "PSD" "PCSK1N" "POLR2I"
## [5] "RASD1" "PDE8B" "TRIM22" "CHI3L1"
## [9] "FHDC1" "WARS1" "ITGA9" "PRSS23"
## [13] "SPOCK1" "CIITA" "WDR97" "IER5L"
## [17] "CARNMT1-AS1" "RP1-223B1.1" "LINC01503" "PRKAR2B-AS1"
## [21] "RP11-745L13.2" "RP1-41C23.1" "PRAG1" "RP11-239A17.1"
## [25] "CTD-2040G12.2" "GAS7" "KLF6" "FRY"
## [29] "TESC" "DNAH11" "TSHZ3" "HELB"
## [33] "COL5A1" "ADAM12" "SEC24D" "COX7A1"
## [37] "PGM2L1" "CCK" "DPYD" "SLC6A9"
## [41] "SMOC1" "MIR34AHG" "RP1-187B23.1" "RP3-365E2.1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_3"
## [1] "NRXN3" "RPH3A" "PEX5L" "UNC13A"
## [5] "CALY" "NDST3" "GRIK2" "FSTL5"
## [9] "NRG4" "MTSS1" "GRIK1" "NEGR1"
## [13] "ERICH3" "CCSER1" "NAP1L3" "CYP4X1"
## [17] "PCLO" "ERC2" "GRM7" "FBXO16"
## [21] "RP11-170M17.1" "MSC-AS1" "CXXC4-AS1" "LINC02217"
## [25] "RP4-809F18.1" "RP11-413N10.3" "RP11-640F22.1" "RP11-320L2.1"
## [29] "RP11-335E8.3" "RIMS1" "SEC14L5" "PDE1A"
## [33] "RIMS3" "NLGN1" "RIMS2" "SYN3"
## [37] "PTPRT" "MMP17" "CYP1B1-AS1" "RP11-147G16.1"
## [41] "LINC01322" "PCAT1" "RP11-4D11.1"
## $go_bp
## category over_represented_pvalue
## 4455 vesicle mediated transport in synapse 2.919111e-11
## 2093 neurotransmitter secretion 1.324490e-10
## 4266 synaptic vesicle exocytosis 2.667018e-10
## 2094 neurotransmitter transport 1.780282e-09
## 3060 regulated exocytosis 3.286610e-08
## 4130 signal release 3.675377e-07
## 882 exocytosis 7.517528e-07
## 3767 regulation of synaptic vesicle exocytosis 2.592537e-06
## 269 calcium ion regulated exocytosis 4.436216e-06
## 3295 regulation of exocytosis 6.453843e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4455 1.0000000 10 29 1.310681e-07
## 2093 1.0000000 9 22 2.973480e-07
## 4266 1.0000000 8 16 3.991637e-07
## 2094 1.0000000 9 29 1.998367e-06
## 3060 1.0000000 8 26 2.951376e-05
## 4130 1.0000000 9 54 2.750407e-04
## 882 1.0000000 8 37 4.821957e-04
## 3767 1.0000000 4 6 1.455061e-03
## 269 0.9999999 5 13 2.213179e-03
## 3295 0.9999997 6 23 2.559716e-03
##
## [1] "set_28"
## [1] "WNT5B" "PDE10A" "F3" "GDAP1L1"
## [5] "TMEM241" "PDE5A" "MEGF11" "HHIP"
## [9] "SEPTIN1" "PNMA3" "SGCZ" "EYS"
## [13] "HES4" "NPSR1-AS1" "KCNMB2" "RP1-292B18.4"
## [17] "SNAP25-AS1" "RP1-45C12.1" "LINC01829" "LINC01618"
## [21] "RP11-673E1.1" "RP11-586K2.1" "AB015752.3" "LINC02389"
## [25] "LINC02254" "RP11-103J8.1" "RP11-314E10.1" "USH2A"
## [29] "RHOBTB1" "LAMB4" "WFDC1" "PXDNL"
## [33] "GREM1" "MRGPRF" "ZNF804B" "FZD9"
## [37] "HRAT92" "LINC02869" "RP11-384F7.1" "LINC01619"
## [41] "CEACAM16-AS1" "PKD1L3" "RP11-93B21.2"
## $reactome
## category over_represented_pvalue
## 130 cgmp effects 6.834660e-06
## 607 nitric oxide stimulates guanylate cyclase 1.541836e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 130 1.0000000 3 6 0.007675323
## 607 0.9999999 3 7 0.008657408
##
## [1] "set_34"
## [1] "ASB4" "MSMO1" "CCDC85A" "IDI1" "SRBD1" "BLVRB"
## [7] "PLS3" "RPL18A" "EPM2A" "GMDS" "LAMA4" "ID2"
## [13] "NID1" "PPP1R3C" "MT2A" "ID1" "IFI6" "APOE"
## [19] "RPL36" "CCDC59" "RPLP1" "FAU" "TEX9" "GFRA1"
## [25] "SYCP2L" "HNF4G" "ALDH1A1" "RPS27" "ZNF48" "GINS3"
## [31] "KIAA0825" "MT1X" "PTMA" "SNHG31" "RPS18" "MRPL33"
## [37] "KNOP1" "ARID3A" "CKB" "MITF" "NOL4L"
## $reactome
## category
## 1078 translation
## 287 eukaryotic translation elongation
## 288 eukaryotic translation initiation
## 610 nonsense mediated decay nmd
## 810 response of eif2ak4 gcn2 to amino acid deficiency
## 878 selenoamino acid metabolism
## 856 rrna processing
## 975 srp dependent cotranslational protein targeting to membrane
## 429 influenza infection
## 527 metabolism of amino acids and derivatives
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1078 1.264399e-07 1.0000000 7 13
## 287 2.368574e-07 1.0000000 6 9
## 288 2.368574e-07 1.0000000 6 9
## 610 2.368574e-07 1.0000000 6 9
## 810 3.470611e-07 1.0000000 6 10
## 878 5.491255e-07 1.0000000 6 10
## 856 6.208334e-07 1.0000000 6 10
## 975 9.426476e-07 1.0000000 6 11
## 429 9.636278e-07 1.0000000 6 11
## 527 1.414785e-06 0.9999999 7 17
## FDR
## 1078 6.649770e-05
## 287 6.649770e-05
## 288 6.649770e-05
## 610 6.649770e-05
## 810 7.794991e-05
## 878 9.959942e-05
## 856 9.959942e-05
## 975 1.202393e-04
## 429 1.202393e-04
## 527 1.588803e-04
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation 3.469051e-07 1
## numDEInCat numInCat FDR
## 618 6 12 0.001557604
##
## [1] "set_38"
## [1] "MT3" "STS" "MT1G" "SUMF1"
## [5] "C2CD6" "STPG2" "CD200R1" "C11orf65"
## [9] "MT1E" "CYP7B1" "SUGCT" "HMGN5"
## [13] "ADD3-AS1" "MT1H" "AC007277.3" "AC004540.5"
## [17] "LINC00571" "MRPS9-AS2" "RP11-162D16.2" "LYPLAL1-DT"
## [21] "ZRANB2-AS2" "LINC01036" "AC079807.4" "RAP2C-AS1"
## [25] "RP11-154D6.1" "SOX2-OT" "RP11-461O7.1" "C1QTNF7-AS1"
## [29] "RP11-124B13.1" "LINC02740" "RP11-727A23.10" "LINC02745"
## [33] "LINC02326" "LINC02327" "LINC02328" "LINC00637"
## [37] "AC007193.6" "RP11-520F22.1" "KBTBD12" "RP11-26J3.1"
## [41] "RP11-150C16.1" "CTD-2201E18.6" "RP3-466I7.2"
## $reactome
## category over_represented_pvalue
## 542 metallothioneins bind metals 6.228691e-08
## 813 response to metal ions 6.228691e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 542 1 4 6 3.49741e-05
## 813 1 4 6 3.49741e-05
##
## $go_bp
## category over_represented_pvalue
## 508 cellular response to zinc ion 4.110986e-08
## 677 detoxification of copper ion 4.110986e-08
## 678 detoxification of inorganic compound 4.110986e-08
## 431 cellular response to copper ion 9.843817e-08
## 4029 response to zinc ion 1.945770e-07
## 3900 response to copper ion 2.004453e-07
## 1214 intracellular zinc ion homeostasis 2.040068e-07
## 423 cellular response to cadmium ion 6.392107e-07
## 3891 response to cadmium ion 6.392107e-07
## 676 detoxification 1.864596e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 508 1 4 6 6.152775e-05
## 677 1 4 6 6.152775e-05
## 678 1 4 6 6.152775e-05
## 431 1 4 7 1.104969e-04
## 4029 1 4 8 1.308558e-04
## 3900 1 4 8 1.308558e-04
## 1214 1 4 8 1.308558e-04
## 423 1 4 10 3.188951e-04
## 3891 1 4 10 3.188951e-04
## 676 1 4 13 8.372037e-04
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955019 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16666322 127.2 31263295 238.6 65536 31263295 238.6
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0